'Nagasaki is the most beautiful city in Japan, more beautiful than even Kyoto," says Bill, an ebullient, baseball-capped American with a fondness for all things Nippon. This is Bill's seventh trip to Nagasaki, but he's looking to get further under the city's skin, so he's joined today's walking tour. It's led by Kaz, an affable fortysomething who's part of a network of volunteer guides keen to show tourists there's more to this city than tragic war stories.

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"Nagasaki has such a long history; such a colourful history," Kaz says. "Too many people think it begins and ends in 1945 with the atomic bomb. We want them to know more."

Megane-bashi bridge on Nakashima River. Photo: Getty Images

We take a breather in Kazagashira Park, a leafy hilltop gem that offers majestic panoramas of the city. Hugging the western tip of Kyushu, the most southerly of Japan's four main islands, Nagasaki is set around a deep harbour and edged by pretty green hills. It has none of the neon-signed, Blade Runner-esque sprawls of Tokyo and Osaka and instead comprises a snug mix of concrete and mirror-glass buildings, wooden temples and shrines, and elegant architecture with a European twist. Trundling through its laid-back - by Japanese standards - streets is a fleet of quaint, colourful trams.

"Much of what you can see down there has been built or reconstructed in the last 50 or 60 years," says Kaz, who then points opposite. "You see that hill? That's Mount Inasa Park. You can take a cable car up there. At night, when everything is lit up, the views are incredible. And you see that hill? Well, on the other side, there's the suburb of Urakami; that's where they dropped the bomb. That's where the real damage was done."

Kaz says he prefers not to dwell too much on the events of August 9, 1945. His father survived the attack and didn't speak about it until he was on his deathbed. I don't argue; this afternoon I'll be heading to Urakami, where museums and memorials expose the gritty details of that savage end to World War II.

We'd begun the tour along the Nakashima river, which meanders through the city to the harbour and is arched by picturesque stone bridges, largely cobbled together by Chinese monks in the 17th century. One is called the Spectacles because of the shape it reflects in the water. The bridges are an example of the strong Chinese influence in Nagasaki.

From the waterfront, we headed into nearby Teramachi, an atmospheric district with its ancient Japanese Shinto shrines, shadowy graveyards and twisting alleys packed with delightful little wooden houses - plus the Sofuku-ji and Kofuku-ji Buddhist temples, which the Chinese monks built in eye-catching Ming dynasty style. The Chinese were responsible for one of Nagasaki's signature dishes, champon - a brothy noodle soup loaded with squid, pork, octopus and vegetables - and some believe they also sparked Japan's first major contact with Europe.

In the mid-16th century, an off-course Chinese ship carrying Portuguese explorers stumbled across Nagasaki, then a small fishing village. After initial scepticism, the Japanese and the Portuguese became trading partners. The Spanish, British and Dutch got in on the act, too, and Nagasaki thrived as a cosmopolitan port city.

Gateway to the West ... Dejima was a base for the Dutch. Photo: Alamy

While Japanese feudal lords were particularly interested in importing European weaponry and Portuguese sweets and sponge cakes (known as castellas), they were less enamoured by the Christian religion and its proselytising missionaries. Slowly, but surely, they crushed this "foreign plague". Christians were arrested, taken to temples and ordered to stamp on statues of the Virgin Mary; public crucifixions took place, the religion was banned and, eventually, under the powerful Tokugawa shogunate, all foreigners were expelled from Japan, bar a small group of Dutch traders considered more interested in business than faith.

This tumultuous period inspired Shusaku Endo's classic novel, Silence - one of a number of books and plays based in Nagasaki. Giacomo Puccini's opera Madama Butterfly is perhaps the most famous; the most recent is David Mitchell's evocative The Thousand Autumns of Jacob de Zoet.

Mitchell's love story is set on Dejima, a man-made island home to the Dutch and, for 250 years, Japan's sole window to the outside world. These days, the old enclave is a tourist attraction, its highlight the Dejima Museum, which exhibits how Western science, art and culture trickled in during the barren years.

Brighter times ... Nagasaki dazzles at night. Photo: Alamy

Japan's period of isolation ended in 1859. Assisted by US Commander Matthew Perry's gunboat diplomacy measures, the West negotiated free-trade treaties. Foreigners returned and their influences are seen amid the hills east of Dejima. There's pretty French-built Gothic-style Oura Catholic Church, and Hollander Slope with its cluster of restored painted wooden Dutch houses. There's also Glover Garden, a splendid hillside villa named after the Scottish merchant Thomas Glover, who sowed the seeds for the country's first railway, founded the Japan Brewery Company (later the Kirin Brewery Company) and also helped Nagasaki become a centre of arms and shipbuilding under the fledgling Mitsubishi Corporation - a status that would lead to its targeting in World War II.

After savouring a bowl of champon and a castella cake for dessert, I tram it to Urakami. Urakami's Atomic Bomb Museum, which lies metres from the bomb's hypocentre, has an array of graphic exhibits, moving accounts from survivors and intriguing details of the manoeuvrings between Allied politicians and military figures.

Three days after the "Little Boy" bomb was dropped on Hiroshima, another port city, Kokura, was to be hit. But when it became shrouded in heavy cloud, the fallback option - Nagasaki - bore the brunt . The "Fat Man" was almost twice as powerful as the "Little Boy". It killed 74,000 people, injured, and in some cases exposed to radiation poison, tens of thousands more and wiped out one-third of the city.

A bitter irony is that Urakami was traditionally Nagasaki's Christian stronghold. Even when the religion was banned, an underground movement here kept it alive. And when Christianity was officially allowed again, Urakami's faithful built a giant cathedral. The bomb destroyed in three seconds what had taken three decades to construct.

It's hard to imagine such carnage as I amble around this peaceful, modern neighbourhood. Sweet scents waft from florists and bakeries, and a group of smiling schoolchildren flock to explore the rebuilt cathedral.

As I continue my travels around Japan, I think back to Nagasaki. Kaz was right. The bomb is just one chapter in the city's gripping story. And I reckon Bill may have been right, too. Nagasaki is the most beautiful city I see in Japan.

Three more things to do in Nagasaki

1 Boat trips Cruise liners dock at Nagasaki's port, but you can also enjoy scenic boat tours around the harbour, with some vessels venturing out to Hashima. Nicknamed Gunkanjima (Battleship Island), it once claimed to be the most densely populated place on Earth, but was abandoned after the closure of its Mitsubishi coalmines in 1974. Hashima's buildings have been ravaged by the elements, giving the island the haunted look of a wrecked battleship.

2 Shimabara A little more than an hour from Nagasaki by train, the castle town of Shimabara was formerly home to feudal lords and samurai warriors. Dotted with carp streams and folk exhibits, plus the longest reclining Buddha in Japan, the town sits on a peninsula in the shadow of Mount Unzen. This active volcano has spawned sulphur pits, steam vents and natural springs, including some enticing onsen (bathing spots). A high-tech museum pays tribute to those who perished in mud slides and lava flows following an eruption in 1991.

3 Going Dutch Labelled "a virtual Holland", Huis Ten Bosch (House in the Forest) is a theme park named after a residence of the Dutch royal family. A 75-minute rail trip from Nagasaki, it has picturesque canals, windmills, tulip gardens, van Gogh exhibitions and Dutch architecture. Hotel Amsterdam is one of several European-style hotels inside this quirky attraction, english.huistenbosch.co.jp.